reconstruct_art_pseudo.h

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/***************************************************************************
 *
 * Authors:     Carlos Oscar Sorzano coss@cnb.csic.es
 *              Slavica Jonic        Slavica.Jonic@impmc.jussieu.fr
 *
 * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
 *
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 2 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
 * 02111-1307  USA
 *
 *  All comments concerning this program package may be sent to the
 *  e-mail address 'xmipp@cnb.csic.es'
 ***************************************************************************/


#include "core/matrix1d.h"
#include "core/matrix2d.h"
#include "core/metadata_vec.h"
#include "core/xmipp_program.h"
#include "core/xmipp_filename.h"

template<typename T>
class MultidimArray;

class ProgARTPseudo: public XmippProgram
{
public:
    FileName fnDoc;

    FileName fnPseudo;

    FileName fnNMA;

    FileName fnRoot;

    double lambdaART;

    int Nit;

    double sigma;

    double sampling;
public:
    void defineParams();

    void readParams();

    void show() const;

    void produceSideInfo();

    void run();

    void writePseudo();

    double ART_single_step(const MultidimArray<double> &Iexp,
        double rot, double tilt, double psi, double shiftX, double shiftY,
        const std::vector<double> &lambda);
public:
    // Input images
    MetaDataVec DF;

    // Atomic positions
    std::vector< Matrix1D<double> > atomPosition;

    // Atomic weights
    std::vector< double > atomWeight;

    // Gaussian projection table
    Matrix1D<double> gaussianProjectionTable;

    // Gaussian projection2 table
    Matrix1D<double> gaussianProjectionTable2;

    // NMA modes
    std::vector < Matrix2D<double> > NMA;
};